chr2-20057095-G-T

Position:

• chr2-20057095-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.161 in 152,166 control chromosomes in the GnomAD database, including 2,554 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.16 (2554 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.20057095G>T		intergenic_region
LAPTM4A-DT	NR_187142.1	n.358+4601G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24414 AN: 152048 Hom.: 2551 Cov.: 32

Gnomad AFR AF: 0.0404

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.0928

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.150

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.161 AC: 24426 AN: 152166 Hom.: 2554 Cov.: 32 AF XY: 0.167 AC XY: 12405 AN XY: 74376

Gnomad4 AFR AF: 0.0403

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.0928

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.148

Alfa AF: 0.166 Hom.: 1209

Bravo AF: 0.145

Asia WGS AF: 0.205 AC: 711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.64

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1513831; hg19: chr2-20256856;